Genotyping all individuals from Viola cheiranthifolia, I found that one population has three alleles for 2 or 3 of the microsatellite markers (16 in total). Repeating the DNA extraction and PCR of the same individuals does not show any difference. Those alleles appear normally in the other populations, with the appearance of a diploid species.
Does anyone have any advice to clarify the posible triploidy of this samples, or to adjust the genotypes?
Thank you in advance for your response
The reason why you observe "triploid" individuals in Viola cheiranthifolia is that the species is not diploid and that you occasionally amplify additional homoeologs. Viola section Melanium is meso-allotetraploid, and the large lineage that V. cheiranthifolia belongs to has undergone at least one more polyploidisation.
There's no easy fix to this problem. However, by sequencing the alleles you may be able to distinguish between homoeologs.
Artur, I mean that in one population, some individuals have more than 2 alleles for some of the markers. In triploid individuals, i think it should happen in the sixteen markers, but I would like to clarify that to avoid genotyping mistakes. The karyotype would definitely help, thank you.
David, I also though about sequencing, but for that i have to run the fragments in a electrophoresis and cut the different alleles, am a I wrong? The markers are trinucleotides and the alleles differ in 3 pb. In agarose gels becomes a challenge...
You can simply use flow cytometry-based procedure or count the chromosome numbers on those 'polyploidy' individual suspects to check out.
The reason why you observe "triploid" individuals in Viola cheiranthifolia is that the species is not diploid and that you occasionally amplify additional homoeologs. Viola section Melanium is meso-allotetraploid, and the large lineage that V. cheiranthifolia belongs to has undergone at least one more polyploidisation.
There's no easy fix to this problem. However, by sequencing the alleles you may be able to distinguish between homoeologs.
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